Although exposed to one of the most pestilential climates in the world, he did not lose a man.
At the breaking out of the Civil War he was in command of the Brooklyn Navy Yard.

He was overwhelmed with work for a time, and was glad when, early in the autumn of 1861, he was ordered to the West to help in the building of an inland navy on the Mississippi.
Captain Foote worked with the tremendous energy which he threw into every task, and succeeded in getting together seven boats, four of which were partly protected by armor.

At the beginning of February, 1862, he started from Cairo to ascend the Tennessee, his objective point being Fort Henry, though the Confederates were deceived into thinking it was Columbus, on the Mississippi.

He asked the Government for more men with which to man additional boats, but they were not furnished, and he went forward with such as he could get.
On the night preceding the attack on Fort Henry the little fleet anchored abreast of the army under General Grant, which was encamped on the bank.

The night was cold and tempestuous, but the morning dawned keen and clear, and no time was lost in preparing the flotilla for the attack on the fort.